Assignment 2 Task 1 Group 19
Alicia Fennell, Amber McEldowney, Jennifer Truong
2/2/2021
Overview
<<<<<<< HEADData for this project comes from Columbia River DART (Data Access in Real Time); the observations used in this project span from January 1, 2001 to December 31, 2010. Adult salmon passage was visually counted and recorded at major dams on Columbia and Snake Rivers.
This report looks at the passage of Coho, Jack Coho, and Steelhead at the Willamette Falls fish ladder in Oregon. Below, we have explored the data using time series plots, seasonplots, and summary statistics and analysis.
Willamette Falls in Oregon. Photo: Willamette Falls Legacy Project
=======- Summary This report explores adult fish passage recorded from 2001-01-01 to 2010-12-31 at the Willamette Falls fish ladder on the Willamette River, Oregon. This report is focused on Coho, Jack Coho, and Steelhead species. First, a time series graph visualized time series data by month and year to explore trends over the 10-year time period. Second, a season plot is created to explore seasonal trends for each species. Lastly, a total counts figure illustrates the total number of observed fish passage for each species over the 10-year period.
Image of Willamette Falls, OR
knitr::include_graphics('willamette_falls.jpeg')
Photo of Willamette Falls, Oregon. Credit: EncMstr, CC BY-SA 3.0 http://creativecommons.org/licenses/by-sa/3.0/, via Wikimedia Commons
Map of Willamette Falls
- A map of the fish ladder location (you can make this in R on your own, or include an existing map appropriately licensed, with attribution) **Figure _.** Location of the fish ladder in Willamette Falls, Oregon.
Citation: Columbia Basin Research. (n.d.). Retrieved February 07, 2021, from http://www.cbr.washington.edu/dart/query/adult_graph_text (I’m using APA format for now, but I’m not a big fan of this…Jen)
Adult Fish Passage at Willamette Falls Fish Ladder
Time series
=======Making tabs (some type of title)
Time series
Need to figure out how to fold code
>>>>>>> master## Read in packages
library(tidyverse)
library(here)
library(janitor)
library(lubridate)
library(tsibble)
## Read in the data, keep only the columns of interest, replace "NA" with 0, and clean names
fish_af <- read.csv(here("data", "willamette_fish_passage.csv")) %>%
select("Date", "Coho", "Jack.Coho", "Steelhead") %>%
mutate_all(~replace(., is.na(.), 0)) %>%
clean_names()
## Convert to tsibble
fish_ts <- fish_af %>%
mutate(date = lubridate::mdy(date)) %>%
as_tsibble(key = NULL, index = date)
## Plot the time series data
<<<<<<< HEAD
# ggplot() +
# geom_line(data = fish_ts, aes(x = date, y = coho)) +
# labs(x = "Date",
# y = "Number of Coho")
## Make data frames for each fish by monthyears
=======
ggplot() +
geom_line(data = fish_ts, aes(x = date, y = coho)) +
labs(x = "Date",
y = "Number of Coho")
## Make data frames for each fish by monthyears
>>>>>>> master
coho_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_coho = mean(coho, na.rm = TRUE))
jack_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_jack = mean(jack_coho, na.rm = TRUE))
steel_month <- fish_ts %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_steel = mean(steelhead, na.rm = TRUE))## Plot time series fish runs
ggplot() +
geom_line(data = coho_month,
aes(x = yr_mo,
y = monthly_mean_coho,
colour = "Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = jack_month,
aes(x = yr_mo,
y = monthly_mean_jack,
colour = "Jack Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = steel_month,
aes(x = yr_mo,
y = monthly_mean_steel,
colour = "Steelhead"),
alpha = 0.7,
size = 1.2) +
labs(x = "Month and Year",
y = "Number of Fish",
colour = "Species",
title = "Adult Passage of Coho, Jack Coho, and Steelhead at Willamette Falls") +
theme_minimal() +
scale_colour_manual(values = c("dodgerblue4", "darkorchid4", "springgreen4")) 
- bullet points summarizing
- trends…
Seasonplots
# Attach feasts package
library(feasts)# Pivot longer
fish_ts_longer <- fish_ts %>%
pivot_longer(2:4,
names_to = "species", # Move each species to its own column
values_to = "n") %>%
group_by(species) %>% # Group by species
index_by(yr_mo = ~yearmonth(.)) %>% # Group by year & month
summarize(monthly_mean = mean(n, na.rm = TRUE)) # Summarize the mean for each species for each month
# Make seasonplot
fish_ts_longer %>%
gg_season(y = monthly_mean)
- bulletpoint 1
- bulletpoint 2
Summary Statistics and Analysis
## Make data frames for each fish species by year
coho_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_coho = sum(coho, na.rm = TRUE))
<<<<<<< HEAD
jack_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_jack = sum(jack_coho, na.rm = TRUE))
steel_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_steel = sum(steelhead, na.rm = TRUE))
=======
jack_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_jack = sum(jack_coho, na.rm = TRUE))
steel_year <- fish_ts %>%
index_by(yr = ~year(.)) %>%
summarize(year_count_steel = sum(steelhead, na.rm = TRUE))
>>>>>>> master
## Plot annual totals for fish passage, for each of the 3 species
ggplot() +
geom_line(data = coho_year,
aes(x = yr,
y = year_count_coho,
colour = "Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = jack_year,
aes(x = yr,
y = year_count_jack,
colour = "Jack Coho"),
alpha = 0.7,
size = 1.2) +
geom_line(data = steel_year,
aes(x = yr,
y = year_count_steel,
colour = "Steelhead"),
alpha = 0.7,
size = 1.2) +
scale_x_continuous(breaks= c(2000,2001,2002,2003,2004,2005,2006,2007,2008,2009,2010)) +
labs(x = "Year",
y = "Number of Fish",
colour = "Species",
title = "Annual Adult Passage of Coho, Jack Coho, and Steelhead at Willamette Falls") +
theme_minimal() +
scale_colour_manual(values = c("dodgerblue4", "darkorchid4", "springgreen4")) 
``` ## Summary - bulletpoint 1 - bulletpoint 2
Figure 1.3 Annual toal Coho, Jack Coho, and Steelhead passage observation were recorded at the Willamette Falls fish ladder on the Willamette River (Oregon) from 2001-2010. Data were shared by and accessed from Columbia River DART (Data Access in Real Time).
Summary
From 2001 to 2010, Steelhead observations showed a steady decline, with a small rebound between 2009-2010.
Coho observations increased drastically, from ~5,000/year to ~25,000/year in 2009.
Jack Coho observations remained relatively consistent over the 10-year period.